[English] 日本語
Yorodumi
- PDB-6smc: mouse Interleukin-12 subunit beta - p80 homodimer in space group P1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6smc
Titlemouse Interleukin-12 subunit beta - p80 homodimer in space group P1
ComponentsInterleukin-12 subunit beta
KeywordsCYTOKINE / homodimer / antagonist / fibronectin / secreted glycoprotein
Function / homology
Function and homology information


Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of smooth muscle cell apoptotic process / positive regulation of T-helper 1 type immune response / interleukin-12-mediated signaling pathway / positive regulation of NK T cell proliferation / T-helper cell differentiation / positive regulation of natural killer cell proliferation / positive regulation of osteoclast differentiation / negative regulation of interleukin-17 production / cytokine receptor activity / natural killer cell activation / response to UV-B / positive regulation of granulocyte macrophage colony-stimulating factor production / negative regulation of interleukin-10 production / defense response to protozoan / positive regulation of interleukin-17 production / positive regulation of activated T cell proliferation / positive regulation of interleukin-10 production / cell surface receptor signaling pathway via JAK-STAT / negative regulation of protein secretion / positive regulation of T cell proliferation / T cell proliferation / positive regulation of defense response to virus by host / positive regulation of interleukin-12 production / cytokine activity / endosome lumen / growth factor activity / negative regulation of smooth muscle cell proliferation / negative regulation of inflammatory response to antigenic stimulus / positive regulation of T cell mediated cytotoxicity / cellular response to type II interferon / Golgi lumen / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / cell migration / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to virus / cell population proliferation / cell surface receptor signaling pathway / endoplasmic reticulum lumen / protein heterodimerization activity / protein-containing complex binding / cell surface / extracellular space / extracellular region / identical protein binding / membrane / cytoplasm
Similarity search - Function
Interleukin-12 beta / Interleukin-12 beta, central domain / : / Cytokine interleukin-12p40 C-terminus / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type III / Fibronectin type III superfamily ...Interleukin-12 beta / Interleukin-12 beta, central domain / : / Cytokine interleukin-12p40 C-terminus / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type III / Fibronectin type III superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-12 subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBloch, Y. / Savvides, S.N.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders12S0519N Belgium
Research Foundation - FlandersG0B4918N Belgium
Research Foundation - FlandersG0E1516N Belgium
CitationJournal: To Be Published
Title: Around she goes: the structure of mouse Interleukin-12 p80
Authors: Bloch, Y. / Savvides, S.N.
History
DepositionAug 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Experimental preparation / Category: database_2 / exptl_crystal_grow
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal_grow.pdbx_details
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interleukin-12 subunit beta
B: Interleukin-12 subunit beta
C: Interleukin-12 subunit beta
D: Interleukin-12 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,66010
Polymers157,5944
Non-polymers3,0666
Water00
1
A: Interleukin-12 subunit beta
C: Interleukin-12 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3305
Polymers78,7972
Non-polymers1,5333
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint8 kcal/mol
Surface area34090 Å2
MethodPISA
2
B: Interleukin-12 subunit beta
D: Interleukin-12 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3305
Polymers78,7972
Non-polymers1,5333
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint11 kcal/mol
Surface area34040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.074, 96.791, 107.780
Angle α, β, γ (deg.)68.586, 76.842, 85.827
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGVALVAL(chain 'A' and (resid 23 through 92 or (resid 95...AA65 - 6865 - 68
12LEULEULEULEU(chain 'A' and (resid 23 through 92 or (resid 95...AA8383
13LYSLYSASNASN(chain 'A' and (resid 23 through 92 or (resid 95...AA217 - 220217 - 220
24ARGARGVALVAL(chain 'B' and (resid 23 through 92 or (resid 95...BB65 - 6865 - 68
25LEULEULEULEU(chain 'B' and (resid 23 through 92 or (resid 95...BB8383
26LYSLYSASNASN(chain 'B' and (resid 23 through 92 or (resid 95...BB217 - 220217 - 220
37ARGARGVALVAL(chain 'C' and (resid 23 through 92 or (resid 95...CC65 - 6865 - 68
38LEULEULEULEU(chain 'C' and (resid 23 through 92 or (resid 95...CC8383
39LYSLYSASNASN(chain 'C' and (resid 23 through 92 or (resid 95...CC217 - 220217 - 220
410ARGARGVALVAL(chain 'D' and (resid 23 through 120 or (resid 121...DD65 - 6865 - 68
411LEULEULEULEU(chain 'D' and (resid 23 through 120 or (resid 121...DD8383
412LYSLYSASNASN(chain 'D' and (resid 23 through 120 or (resid 121...DD217 - 220217 - 220

-
Components

#1: Protein
Interleukin-12 subunit beta / IL-12B / Cytotoxic lymphocyte maturation factor 40 kDa subunit / CLMF p40 / IL-12 subunit p40


Mass: 39398.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Residues 1:22 form the signal peptide and should be cotranslationally cleaved.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il12b / Plasmid: pHLsec / Cell line (production host): HEK293S GlycoDelete / Production host: Homo sapiens (human) / References: UniProt: P43432
#2: Polysaccharide
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Cl
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 200 MM NAFORMATE, 100 MM NAPO4 PH 6.2, 10 % GLYCEROL, 20% MEDIUM PEG SMEAR (BCS CONDITION 40)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.5→48.76 Å / Num. obs: 21609 / % possible obs: 92.9 % / Redundancy: 4.12 % / Biso Wilson estimate: 119.7 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.233 / Net I/σ(I): 5.49
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
10.28-48.764.0523.468210.9960.05889.6
7.35-10.284.1516.515510.9970.07597.1
6.02-7.354.29.4619540.9880.14995.6
5.23-6.024.026.9322820.9880.19193.9
4.68-5.234.115.6924380.9840.23590.1
4.28-4.684.144.0627770.9510.36891.6
3.96-4.284.182.4630560.8920.62392.4
3.71-3.964.171.2832850.7291.117394
3.5-3.714.090.7734450.5781.85291.9

-
Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.16_3549refinement
XDS20190315data reduction
XDS20190315data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SFF

6sff


Resolution: 3.5→48.76 Å / SU ML: 0.5686 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 37.1363
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3098 2153 10.03 %
Rwork0.2787 19316 -
obs0.2818 21469 92.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 153.31 Å2
Refinement stepCycle: LAST / Resolution: 3.5→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9582 0 202 0 9784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003210005
X-RAY DIFFRACTIONf_angle_d0.682213568
X-RAY DIFFRACTIONf_chiral_restr0.04481521
X-RAY DIFFRACTIONf_plane_restr0.00491719
X-RAY DIFFRACTIONf_dihedral_angle_d2.55286032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.580.38911460.42841218X-RAY DIFFRACTION86.17
3.58-3.670.40981450.40071260X-RAY DIFFRACTION95.38
3.67-3.770.41181570.42111332X-RAY DIFFRACTION95.76
3.77-3.880.40981240.39941344X-RAY DIFFRACTION93.15
3.88-4.010.39661610.35451264X-RAY DIFFRACTION93.63
4.01-4.150.32111370.32221326X-RAY DIFFRACTION93.42
4.15-4.320.32891290.28981249X-RAY DIFFRACTION91.56
4.32-4.510.35081490.31271285X-RAY DIFFRACTION92.16
4.51-4.750.30851330.27841250X-RAY DIFFRACTION90.87
4.75-5.050.31251410.24921242X-RAY DIFFRACTION89.51
5.05-5.440.28611360.24911270X-RAY DIFFRACTION91.06
5.44-5.980.2931490.26571314X-RAY DIFFRACTION94.88
5.98-6.850.29831490.27241326X-RAY DIFFRACTION95.84
6.85-8.620.29921510.24711354X-RAY DIFFRACTION97.1
8.62-48.760.2331460.19911282X-RAY DIFFRACTION92.61
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.479393458733.45403354322.318054382055.205548766691.818869284493.330057795660.1118336357010.29915242327-0.0836508728087-0.100784403135-0.00428229736590.5219575284660.368987134933-0.0796702069744-0.03866033535541.16675796598-0.129260800057-0.283952880340.7770735697570.2679841052351.3018279510351.0950418137-19.784475863654.9220226324
24.311855996721.797041221410.976078831993.692152229861.181548983072.97518786095-0.0302493030088-0.1913435191040.2411416881050.2009199103190.0290213252502-0.0443983156542-0.301841415860.3363558342910.0180131209410.994900365224-0.0333563965747-0.324750516740.6519607969420.2165032193471.18073285108-18.78525107196.56686254495-25.2151075872
33.247930389920.4211653224733.121938708231.278740611030.8129531235946.85987325963-0.02433430964570.54786069694-0.165654904406-0.2896861667440.1845299471170.533329320468-0.0586335314384-0.270125772054-0.1742796701381.35459906966-0.172641697652-0.5213323497390.928755540350.2302393447151.625673927148.265417694726.135129298332.2198151371
44.103758627210.2427280615651.159136613381.0058995251-0.01014905672121.198684525480.17728648732-0.318017908725-0.4983176190870.51831525810.0553039890163-0.3296220242790.2678460737360.192696085273-0.2028451466721.75639314176-0.183885642455-0.6489942737061.155279211710.3626711110031.5847588293-20.8083025313-35.97742876622.34432234636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain B
3X-RAY DIFFRACTION3Chain C
4X-RAY DIFFRACTION4Chain D

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more